Make DG fields in the restart file self-consistent

[timspainNERSC]

Currently, the thermodynamics runs after the dynamics. Since the thermodynamics changes the mean, DG0 value of prognostic fields, this can mean that the higher DG components could be such that the value of the field exceeds its physical limits. To be fully consistent the final state of fields with both DG components and geophysical limits should be immediately after the dynamics, when the limiters have just been applied.

The solution to this would be to swap the order of the dynamics and thermodynamics within the PrognosticData::update().